Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rxra

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
RXR_Male_Vehicle_27hr_Liver
strain
CD-1 (Charles River)
Sex
male
age
8 weeks
treatment
Vehicle (1% DMSO in corn oil)_ 27 h
tissue
liver
chip antibody
RXRa (Santa-Cruz Biotechnology #SC-553)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was extracted from frozen liver tissue from each of the individual livers per group. Crosslinking was achieved by adding formaldehyde to a final concentration of 1% for 5 min at room temperature. ChIP was performed using the following ChIP-validated antibodies: RXRa (Santa-Cruz Biotechnology #SC-553), CEBPa (Santa-Cruz Biotechnology #SC-61), CEBPb (Santa-Cruz Biotechnology #SC-150). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB, catalog no. E7645) according to the manufacturer's instructions. NEBNext Multiplex Oligos for Illumina (NEB, Set 1; catalog no. E7335, NEB, Set 2; catalog no. E7500) were used for multiplexing. Samples marked input control correspond to sequencing libraries from sonicated chromatin that was not subject to ChIP.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
21249678
Reads aligned (%)
96.9
Duplicates removed (%)
13.2
Number of peaks
12867 (qval < 1E-05)

mm9

Number of total reads
21249678
Reads aligned (%)
96.7
Duplicates removed (%)
13.9
Number of peaks
12850 (qval < 1E-05)

Base call quality data from DBCLS SRA